The Convergence of Infectious Diseases and Noncommunicable Diseases Proceedings of a Workshop (2019) / Chapter Skim
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5 Microbial Dimension to Human Development and Well-Being
5 Microbial Dimension to Human Development and Well-Being
Pages 51-64
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From page 51... ...
The efforts of the Human Microbiome Project (HMP) have revealed that each human has around 20,000 human genes,1 a measly comparison to the 2 to 20 million microbial genes in human bodies (Knight et al., 2017; NIH, 2019)
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From page 52... ...
Because these microbial genes encode the vast majority both of unique biochemical functions and of antigens, this type of work ignores the genes that can be changed and modified throughout humans' lifetimes to promote health and rather focuses instead on the 1 percent that are fixed when humans are conceived. GLOBAL MICROBIAL BIODIVERSITY CRISIS Despite the significant number of microbial genes in humans, however, humans are losing them (Smits et al., 2017)
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From page 53... ...
. More recently, other scientists documented similar effects when humans eliminate microbes early in life and thus affect the inner human ecosystem, which may be growing into a biodiversity crisis (Blaser, 2014)
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From page 54... ...
Knight added that although the microbiomes included on the map come from healthy people, many factors can affect the microbiome, including age, gender, the time of day the sample was collected, and what the person ate the day before. To build this evidence base, the Earth Microbiome Project,2 which aims to characterize global microbial taxonomic and functional diversity on Earth, crowdsourced tens of thousands of samples from scientists around the world (Gilbert et al., 2014)
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From page 55... ...
The way a person is born has a huge effect on those microbial origins. Babies delivered vaginally have microbial communities similar to their mother's vaginal microbe communities, but the starting point is completely different for babies delivered via cesarean section, who have communities throughout their bodies that are all similar to their mother's specific skin communities (Dominguez-Bello et al., 2010)
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From page 56... ...
It could also be used to predict the effect of falling off the microbiome "growth curve," he added. RESEARCH DIRECTIONS TO EXPLORE MICROBIOME COMPLEXITY Knight described some of the research directions that could help provide a more realistic understanding of this complex relationship of microbes to infectious diseases, NCDs, and normal physiological functioning.
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From page 57... ...
To contribute more robust research and an integrated picture of diet, microbiology, and immunity, Knight has cofounded the Global FoodOmics Project, which is running thousands of food samples through a mass spectrometer to find out what is in food products at the point of sale or at the point of consumption.3 These data are cross-referenced with the American Gut Project, which has collected more than 20,000 stool samples contributed by citizen scientists, as well as performing meta-analyses with their other clinical projects.4 He presented a picture of a molecular network from an early iteration of the project, which reveals the complete biotransformation of food in the human gut. In new mouse models, researchers have been 3D scanning conventionally raised, pathogen-free, and germ-free mice, then dicing them to sequence and running the mass spectrometer on each piece.
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From page 58... ...
Knight called for a coordinated global effort to build a more comprehensive repository of information about the microbiomes of people with much more diverse demographic, geographical, and health-related characteristics. This effort should be catalyzed by the potential strides to be made against the sheer number of conditions that have now been linked to the gut microbiome, such as inflammatory bowel disease, irritable bowel syndrome, food allergies, asthma, cardiovascular disease, diabetes, multiple sclerosis, autism, and Parkinson's disease, he said.
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From page 59... ...
In his concluding remarks, Knight described his vision of future tools to track the microbiome (see Box 5-1) and outlined a set of research needs, including the following: • More work integrating food, drugs, microbiology, immunology in studies with multiple data layers and large enough study popula tions to get adequate statistical power • More comparative studies of microbiomes in populations where burdens of infectious and chronic disease differ BOX 5-1 Future Tools for Personalized Microbiome Tracking Knight described his vision of future molecular and data science tools for tracking the microbiome.
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From page 60... ...
Factors Shaping the Human Microbiome Srinath Reddy, president of the Public Health Foundation of India, asked about the nature of epigenetic changes in the microbial genes and long-term effects beyond changing the character of the colony, as well as whether environmental exposures are more likely to lead to epigenetic changes in the huge pool of genes in the microbiome. Knight replied that little is known about the epigenetics of the bacteria, but there is evidence of the epigenetic process of DNA methylation in the bacterial genomes themselves.
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From page 61... ...
Kevin Olival, senior research scientist at EcoHealth Alliance, asked about the role of viruses, particularly bacterial phages, in shaping human microbial communities. Knight replied that the prospect of understanding phage bacterial dynamics is exciting.
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From page 62... ...
He added that stool is more practical for daily sampling in longitudinal studies, because variation in the microbiome itself -- even on a daily time scale -- allows for predicting future-state immunologically linked phenotypes such as inflammatory bowel disease. Public Health Implications of Microbiome Research Jay Varma, senior advisor at the Africa Centres for Disease Control and Prevention, asked if microbiome research corroborates the current "super foods" trend and claims about how diet can boost a person's immunity.
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From page 63... ...
To make this type of data useful and actionable at the individual level, he said, will require input from federal agencies and others to develop standards for integrating individual samples into consistent reference ranges, as well as work to standardize databases across specific geographical locations.
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